Check the Device Profile (Tools > Options > Portable Device Sync in MMW) and make sure the files aren't part of some selection to be synced. This generally ends up being the case.

I've been using MediaMonkey (for Windows) for a while now to manage my audio library and to sync selected songs and audiobooks with my Galaxy S8. Everything worked fine until I recently added a bunch of audiobooks. I unselected most of them in the Auto-Sync settings since my Galaxy's storage isn't large enough for all of them. Now when I want to sync my library, MediaMonkey tries to copy all of the new audiobooks to my Galaxy. This takes forever since I use WiFi for syncing (I have an unresolved USB disconnection issue) and at the end the dialog tells me that some files failed to sync since my device runs out of storage space. I tried selecting and unselecting the new audiobooks several times without success. All unselected audiobooks I had before adding the new ones do not get synced. Did anybody run into a similar problem and can offer help? Thanks in advance!